Even when setting the camera to manual, you can get small shifts in exposure as closing the diaphragm by the camera is not 100% precise (Chasseur d'Images was testing this many years ago, and differences could be about 0.2EV). Furthermore light can evolve fast in the conditions you shot the panorama.

That said, the panorama software's today are normally correcting for those slight exposure differences between consecutive shots, and it's a long time I did not see such obvious seams! However I never tried with nefs, always jpegs... Maybe try to convert to jpegs before running the stitcher like DANdeMAN suggested?